Upgrades that require service interruption are announced before they occur. This event was not, and yet Cryptsy announced after the exchange went haywire that it was an upgrade. Either they are lying about it being an upgrade, or they are incompetent idiots who would not warn customers before stopping service. Believe what you like.
With all the backlash cryptsy has received from us lately I'd understand why they wouldn't want to announce site-wide maintenance prior to it happening. How would that stop people like you spreading fud? For an exchange that has never been reportedly hacked, I'd say that Cryptsy is on a pretty good standing.